{ "type": "genome", "identifier": "GCF_009762795.1", "organism": "Pseudodesulfovibrio cashew", "title": "Pseudodesulfovibrio cashew", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CHINESE ACADEMY OF SCIENCES", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009762795.1", "bioproject": "PRJNA224116", "biosample": "SAMN13382117", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2678688", "species_taxid": "2678688", "organism_name": "Pseudodesulfovibrio cashew", "infraspecific_name": "strain=SRB007", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/18", "asm_name": "ASM976279v1", "asm_submitter": "CHINESE ACADEMY OF SCIENCES", "gbrs_paired_asm": "GCA_009762795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/762/795/GCF_009762795.1_ASM976279v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3909950", "genome_size_ungapped": "3909950", "gc_percent": "60.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009762795.1-RS_2024_04_05", "annotation_date": "2024-04-05", "total_gene_count": "3600", "protein_coding_gene_count": "3523", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-18", "dateModified": "2019-12-18", "datePublished": "2019-12-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudodesulfovibrio cashew" ], "sample_taxid": [ "2678688" ], "sample_host_organism": [ "cashew" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Nanhai" ], "sample_host_location_id": [], "data_size": "1.097 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3909950", "Number of Sequences": "1", "Longest Sequences (bp)": "3909950", "N50 (bp)": "3909950", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.9", "Number of CDSs": "3611", "Average Protein Length": "318.4", "Coding Ratio (%)": "88.2", "Number of rRNAs": "9", "Number of tRNAs": "55", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudodesulfovibrio cashew", "strain": "strain=SRB007", "accession": "GCA_009762795.1", "taxid": 2678688, "species_taxid": 2678688, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1302, "total_fragments": 1303, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudodesulfovibrio indicus", "strain": "strain=J2", "accession": "GCA_001563225.1", "taxid": 1716143, "species_taxid": 1716143, "relation_to_type": "type", "validated": true, "ani": 81.5771, "matched_fragments": 723, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio indicus", "strain": "strain=DSM 101483", "accession": "GCA_004365595.1", "taxid": 1716143, "species_taxid": 1716143, "relation_to_type": "type", "validated": true, "ani": 81.5666, "matched_fragments": 732, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio mercurii", "strain": "strain=ND132", "accession": "GCA_000189295.2", "taxid": 641491, "species_taxid": 641491, "relation_to_type": "type", "validated": true, "ani": 81.5148, "matched_fragments": 725, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio hydrargyri", "strain": "strain=BerOc1", "accession": "GCA_001874525.1", "taxid": 2125990, "species_taxid": 2125990, "relation_to_type": "type", "validated": true, "ani": 81.4668, "matched_fragments": 742, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio aespoeensis", "strain": "strain=Aspo-2", "accession": "GCA_000176915.2", "taxid": 182210, "species_taxid": 182210, "relation_to_type": "type", "validated": true, "ani": 80.576, "matched_fragments": 627, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio alkaliphilus", "strain": "strain=F-1", "accession": "GCA_009729555.1", "taxid": 2661613, "species_taxid": 2661613, "relation_to_type": "type", "validated": true, "ani": 79.6709, "matched_fragments": 522, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio profundus", "strain": "strain=500-1", "accession": "GCA_900217235.1", "taxid": 57320, "species_taxid": 57320, "relation_to_type": "type", "validated": true, "ani": 79.1565, "matched_fragments": 381, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio sediminis", "strain": "strain=SF6", "accession": "GCA_020886695.1", "taxid": 2810563, "species_taxid": 2810563, "relation_to_type": "type", "validated": true, "ani": 79.0491, "matched_fragments": 445, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudodesulfovibrio tunisiensis", "strain": "strain=RB22", "accession": "GCA_022809775.1", "taxid": 463192, "species_taxid": 463192, "relation_to_type": "type", "validated": true, "ani": 78.5292, "matched_fragments": 391, "total_fragments": 1303, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009762795.1", "gtdb_species": "s__Pseudodesulfovibrio cashew", "ani": 100.0, "matched_fragments": 1303, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCF_001563225.1", "gtdb_species": "s__Pseudodesulfovibrio indicus", "ani": 81.5857, "matched_fragments": 721, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000189295.2", "gtdb_species": "s__Pseudodesulfovibrio mercurii", "ani": 81.5277, "matched_fragments": 724, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001874525.1", "gtdb_species": "s__Pseudodesulfovibrio hydrargyri", "ani": 81.4471, "matched_fragments": 745, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_015709315.1", "gtdb_species": "s__Pseudodesulfovibrio sp015709315", "ani": 81.1882, "matched_fragments": 605, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_017351175.1", "gtdb_species": "s__Pseudodesulfovibrio sp017351175", "ani": 80.6168, "matched_fragments": 637, "total_fragments": 1303, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio", "ani_circumscription_radius": 95.0, 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"coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Pseudodesulfovibrio", "cashew" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }